Taxonomic profiling of bacterial and archaeal communities from saliva, stool, and CapScan-sampled gut metagenomes

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Subject: OD

Envivo Bio, Inc.; Confidential

1.1 Overview of microbial community composition

Figure 1 is an interactive figure showing the microbial community composition in each collected sample. Here, each color and shade corresponds to a different genus. For reference, domestic dogs (Canis familiaris) and gray wolves (Canis lupus) are different species that belong to the same genus (Canis).

You can interact with this figure by:

• Hovering the cursor over a color in the stacked bar to see the taxonomic identity, sample type, and relative abundance corresponding to that color and bar
• Clicking and dragging the cursor over a portion of the figure to zoom
• Single-clicking a genus’s name in the legend to remove that genus from the figure
• Double-clicking (very quickly) a genus’s name in the legend to only show that genus

Figure 1: Microbial community composition of collected saliva, stool, and CapScan samples. CapScan samples are ordered from proximal to distal intestine (i.e., increasing distance from mouth). Taxonomic composition is reported at the genus rank. Genera present at <1% relative abundance across all samples are reported as “Other genera”. Note: Blue = Firmicutes; Yellow = Actinomycetes; Green = Bacteroidetes; Red = Proteobacteria; Purple = all other phyla. Shades of the same color (except purple) correspond to different genera from the same phylum.

1.2 High-resolution snapshot of community composition

Figure 2 is an interactive figure showing the microbial community composition at higher taxononomic resolution. Here, each row corresponds to a unique microbe.

You can interact with this figure by:

• Hovering the cursor over a cell to see that microbe’s genus and species (and strain when available), relative abundance, and full taxonomic classification
• Clicking and dragging the cursor over a portion of the figure to zoom

Figure 2: Heat map showing relative abundance of microbes in each sample (N = 148 total identified). Each row corresponds to a unique microbe and each column corresponds to an individual sample. Note the relative abundance colorscale is in log units.

1.3 Notable microbes detected

• Bifidobacterium stercoris:
  • Previously isolated strains shown to produce gamma-aminobutyric acid (GABA) (Duranti et al., 2020), a compound that plays a role in mitigating anxiety and depressive disorders
  • Composed 1-5% of CapScan-sampled microbial communities
  • Note: Renamed Bifidobacterium adolescentis in 2013 (Killer et al., 2013)
    
    
• Evtepia gabavorous:
  • Previously isolated strain shown to metabolize GABA, likely using it as a carbon and energy source (Strandwitz et al., 2019)
  • Composed 1-2% of CapScan-sampled microbial communities

1.4 References

Duranti, S., Ruiz, L., Lugli, G.A., Tames, H., Milani, C., Mancabelli, L., et al. (2020) Bifidobacterium adolescentis as a key member of the human gut microbiota in the production of GABA. Sci Rep 10: 1–13.

Killer, J., Sedláček, I., Rada, V., Havlík, J., and Kopečný, J. (2013) Reclassification of Bifidobacterium stercoris Kim et al. 2010 as a later heterotypic synonym of Bifidobacterium adolescentis. Int J Syst Evol Microbiol 63: 4350–4353.

Strandwitz, P., Kim, K.H., Terekhova, D., Liu, J.K., Sharma, A., Levering, J., et al. (2019) GABA-modulating bacteria of the human gut microbiota. Nat Microbio 4: 396–403.